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25 Cards in this Set
- Front
- Back
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What is a buffer?
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A solution that resists changes in pH. Usually consists of a weak acid and its conjugate base.
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What is the buffer zone, and the equivalence point?
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The buffer zone is the zone on a pH titration curve that is usually less steep than the rest of the graph, because the buffer is resisting change in pH. The weak acid is being converted to conjugate base, taking the additional OH ions in suspension, disallowing them to contribute to pH change.
The equivalence point is the point within a buffer zone in which the weak acid equals the conjugate base. At this point, the pH equals pKa of species of interest. |
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What is the henderson-hasselbalch equation?
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pH = pKa + log(A-/HA)
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Charged Polar AA's:
How many What are they |
5
Histidine Arginine Lysiene Glutamic Acid Aspartic Acid |
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Uncharged, Unpolar AA's:
How many What are they |
9
VAG LIP MPT Valine Alanine Glyciene Leucine Isoleucine Proline Methionine Phenylalanine Tryptophan |
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Uncharged, Polar Amino Acids
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STAG CT
Serine Tyrosine Asparagine Glutamine Cysteine Threonine |
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Properties of the Peptide Bond
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C=O and N (Amide)
Planar Limited rotation around Phi and Psi Rigid Trans configuration |
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Definition of:
1. Phi angle 2. Psi angle |
1. alpha carbon and NH2
2. alpha carbon and COOH |
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Nonstandard amino acid
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Modification of an amino acid residue after it has been incorporated into a polypeptide.
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Significance of primary structure
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Contains all information for peptide chain folding into "native" structure
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What is the [A-] /[HA] ratio when the weak acid is in a solution one pH unit above its pKa?
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10:1
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Know the structure of the alpha helix and the importance of the amino acids, H-bonds
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Right handed corkscrew in nature.
Hydrogen bonds between the C=O group of Ci and the NH group of Ci+4 Schematic drawing: ribbon |
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Know the structure of B sheets, and importance of amino acids, H-bonds
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Parallel sheets: Adjacent B strands run in the same direction. Hydrogen bonds connect each amino acid on one strand with two different amino acids on the adjacent strand.
Antiparallel sheets: Adjacent B strands run in opposite directions. Hydrogen bonds connect each amino acid to a single amino acid on adjacent strand, stabilizing the structure. Schematic drawing: broad arrows |
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Know and be able to discuss difference between globular and fibrous proteins
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Fibrous proteins, such as alpha keratin and and collagen, consist only of secondary structure, and are insoluble.
Globular proteins have tertiary and quaternary structure and are soluble. |
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Supersecondary structure, or motifs
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Combinations of secondary structures.
EX: Two helices separated by a turn is called a helix-turn-helix motif |
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Domain?
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When polypeptide chains fold into two or more compact regions that may be connected by a flexible segment of polypeptide chain, kind of like pearls on a string. The compact globular units are called domains.
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4 levels of protein structure, differences, bonding interactions
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1. Primary - the sequence of amino acids. Determines the native structure. Held together by peptide bonds.
2. Secondary. Alpha helix or beta sheets. Held together by hydrogen bonds. 3. Tertiary. The 3d shape of folded protein. Held together by hydrophobic interactions Electrostatic interactions Hydrogen Bonds Chemical Cross Linking 4. Assembly of two or more tertiary proteins. |
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Disease from protein misfolding
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Mad Cow Disease
Transmitted from Prions Normal proteins in brain PrP are normally Alpha helix. When prion is introduced, it is a misfolded protein that is in the form of a beta sheet. Then, other proteins aggregate onto it, forming an aggregate called an amyloid form. |
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How do you reversibly cleave a disulfide bond?
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With beta-mercaptoethanol, of course!
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The most common AA's in:
1. Alpha helices 2. Beta sheets 3. Reverse Turns |
1. Alanine, glutamate, leucine
2. Valine, threonine, isoleucine (branching at the beta carbon) 3. Proline, Glycine, Asparagine |
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How to extract pure proteins from a cell
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Disrupt the cells via homogenization, then use differential centrifugation to separate based on density.
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What is column chromatography
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column is full of gel interspersed with beads. Small molecules travel slower because they become trapped in the beads. Larger molecules travel faster because they do not get trapped in the beads. Thus, protein is separated based on size, with bigger coming out first.
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What is electrophoresis
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apply sds to give all protein a negative charge. Then, place in loading gel, flip the switch, turn on the juice, the protein will then move through the gel and will isolate proteins based on size.
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How do we determine primary structure of a protein?
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Edman degradation
Removes one amino acid at a time from the N terminus Pros: process is automated works with peptides of up to 50 residues Cons: Not 100% yield Must cleave stuff that's over 50 AA's long Disulfide bonds present problems 1st: determine amino acid composition. Break apart peptide bonds by heating in 6M HCl at 110 degrees celsius for 24 hours. Separate the amino acids in hydrosylate by ion-exchange chromatography. Identity revealed by elution volume. |
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Sequence specific cleavage:
1. trypsin 2. chymotrypsin 3. CNBr |
1. Carboxyl side of lys and arg residues
2. carboxyl side of tyr, trp, phe, leu, met 3. carboxyl side of met |
